[Biopython-dev] Biopython new release coming up

Michiel De Hoon mdehoon at c2b2.columbia.edu
Thu Oct 20 16:08:57 EDT 2005

Thanks, Peter!
I have added these files to CVS and written a simple test_NCBIXML.py for it
(also in CVS).


Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032

-----Original Message-----
From: Peter [mailto:biopython-dev at maubp.freeserve.co.uk]
Sent: Thu 10/20/2005 1:40 PM
To: Michiel De Hoon
Cc: biopython-dev at biopython.org
Subject: Re: [Biopython-dev] Biopython new release coming up
Michiel De Hoon wrote:
> Hi everybody,
> It's been a while since our latest Biopython release. I'm planning to put
> together a new release (version 1.41, code-named "Manhattan") and hoping to
> release it by the end of next week. So if you have some code sitting around
> that is stable enough for a Biopython distribution, this would be a good
> to commit it to CVS.
> Currently, the following tests fail:

In BioPython 1.40b there where no tests of NCBIXML.py

Do any of you have a collection of XML blast output?

Ideally the test set should cover both the online and standalone 
versions of blast, the different programs (blastn, blastp etc), and a 
range of recent releases (e.g. 2.2.10 to 2.2.12 say).

I have prepared a set of XML from the current blast webserver, attached 
to this email:

'xbt001', # BLASTP 2.2.12, gi|49176427|ref|NP_418280.3|
'xbt002', # BLASTN 2.2.12, gi|1348916|gb|G26684.1|G26684
'xbt003', # BLASTX 2.2.12, gi|1347369|gb|G25137.1|G25137
'xbt004', # TBLASTN 2.2.12, gi|729325|sp|P39483|DHG2_BACME
'xbt005', # TBLASTX 2.2.12, gi|1348853|gb|G26621.1|G26621, BLOSUM80

[I assume the existing tests are bt### for blast test ###, so mine are 
xbt### for XML blast test ###]

I have also attempted to create a test_NCBIXML.py based on Jeffrey 
Chang's test_NCBIStandalone.py but most of it doesn't seem to apply 
(e.g. there is no _scanner, and as far as I can tell, 
rec.multiple_alignment does not apply to XML blast data).

Any comments?

Once this is pinned down, I want to try and try dealing with some 
RPS-BLAST XML output with NCBIXML.py...


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